The Big Tujunga Wash, among Southern California’s most powerful and least developed rivers, is at ground zero of a growing political battle over the route the California bullet train would take as it enters the Los Angeles basin.

The wash carries more than 5 billion gallons per year along a section that has endangered species, protected habitat, parks and equestrian trails. In big winter storms, giant boulders roll down the river bed, attracting spectators to its banks.

It is here — at the junction of Shadow Hills, Lake View Terrace and other small enclaves of the northeast San Fernando Valley — that the California High Speed Rail Authority may build a quarter-mile-long elevated viaduct, allowing trains to exit a long tunnel through the San Gabriel Mountains as they head toward a future station in Burbank.

But the plan is attracting growing scrutiny by government boards and local citizen groups, who are urging the state to eliminate the route from consideration and instead continue developing an alternative plan that would have the trains approach Burbank in a continuous long tunnel.

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The Los Angeles City Council and the Los Angeles Unified School District in the last week have taken initial steps toward adopting motions and resolutions opposing the route, known by the authority as the E2 route. The actions follow a resolution earlier this summer by the Los Angeles County Board of Supervisors to formally oppose the E2 route.

The bullet train project, which plans to someday connect Los Angeles to San Francisco with 220-mph trains, has always faced a tough problem with getting a rail line into Los Angeles. In its business plan adopted earlier this year, it punted the problem down the road and said it would be the last segment it would build, if it can find a source for about $43.5 billion that it does not now have.

The journey from Bakersfield in the Central Valley to Burbank will require about 36 miles of underground passage, the most challenging tunneling project in the nation’s history.

The San Gabriel and Tehachapi mountains are geologically complex, consisting of billion-year-old rocks that have been folded, fractured, tumbled and metamorphosed. They are laced with faults capable of generating powerful earthquakes. And aquifers can deliver high water pressures through fissures in the rock.

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The rail authority is boring five exploratory wells through the rock above the San Fernando Valley in an effort to understand the challenge, and community groups and cities are urging the state to put more of the route underground to avoid impacts in developed neighborhoods. The state abandoned the aboveground E3 route last year.

But the remaining E2 route, some of which is also aboveground, is just as controversial. The route would reverse the city’s costly efforts to restore natural habitat to the Los Angeles River system, displace a couple hundred businesses, remove as many as 100 homes and impact half a dozen schools, opponents say.

Los Angeles is spending billions of dollars to restore other sections of the river that will never be as pristine as the Big Tujunga Wash, and putting a large concrete structure across it would be moving in the entirely wrong direction, said Karo Torossian, director of planning and environment for City Councilman Paul Krekorian.

Krekorian authored the motion opposing the E2 route and was seconded by Council President Herb Wesson.

“We are spending billions of dollars to restore the river in areas that will not be nearly as nice as this part of the river,” Torossian said.

Meanwhile, Los Angeles school board member Monica Ratliff introduced a resolution that would oppose E2, in part because it would pass within 1,500 feet of four public elementary schools and two high schools. In an interview, Ratliff said she is concerned about noise and dust during years of construction, as well as the noise from future operation of the trains through the community. She singled out Brainard Elementary, a small school in Lake View Terrace that had relatively poor tests scores but has shown dramatic progress in tripling the percentage of students meeting standards.

“I do not believe the school would survive the negative impacts of the E2 route,” she said. The school board is scheduled to vote on the resolution next month.

It is not likely that the rail authority is going to easily back down. Spokeswoman Lisa Marie Alley asserted that the authority is not facing opposition.

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“The California High-Speed Rail Authority has a very good working relationship with the L.A. County Board of Supervisors, the L.A. City Council and the mayor of Los Angeles,” she said.

But the authority’s handling of the E2 route is generating some distrust. Part of the controversy involves whether the rail authority openly disclosed that one of its two sites for a “Burbank” station actually is in the city of Los Angeles.

Though the passenger terminal is in Burbank, the 1,400-foot train platform where passengers enter and depart trains would be mostly in the city of Los Angeles. The rail authority granted Burbank a nearly $1-million station-planning grant. Now, Krekorian in his motion wants the rail authority to sign a station-planning grant with Los Angeles that would cover engineering, planning and environmental costs.

In an email, Alley, the authority spokeswoman, disputed that the station is in Los Angeles, apparently referring to the passenger terminal. In addition, Alley notes that the rail authority has other cooperative agreements with the city. Krekorian’s staff, which learned about the location in Los Angeles only in the last few months, insists that the platform is the essential part of any station.

The discrepancy was discovered by the group Save Angeles National Forest for Everyone and raised at a community meeting.

“It was absolutely a political blunder by the rail authority,” said David DePinto, one of the group’s cofounders. “They didn’t disclose it until they were asked. This is par for the course with these guys.”

The continuing problems with finding an acceptable route are leading to proposals that the rail authority simply use the existing Metrolink corridor, which has a twisty right of way from Burbank to Palmdale.

“The best bang for the buck is to stick with the existing Metrolink right of way,” said Glendale City Councilman Ara Najarian, who is a member of the Metropolitan Transportation Authority board and the Metrolink board. “The existing plan is very expensive for a project that is already financially burdened.”

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Such a plan would put Southern California on par with the Bay Area, which succeeded in defeating the rail authority’s intent to build separate tracks through the wealthy peninsula communities of Silicon Valley. The compromise meant that future trains will have to share tracks at slower speeds with commuter trains.

The rail authority has said it would select a route by next year, a decision that will undoubtedly depend to some extent on Los Angeles Mayor Eric Garcetti, who has said little publicly on the matter.